Papova viruses

Papova viruses

1. Papovaviruses By- Sanju Sah St. Xavier’s College, Maitighar , Kathmandu Department of Microbiology

2. Family papovaviridae comprises two genera : The genus Papillomavirus, containing the many papillomaviruses of mammals and birds, The genus Polyomavirus, containing a few pathogens of animals and humans.  The first two syllables of the name Papovaviridae refer to the genera Papillomavirus and Polyomavirus; "va" alludes to "vacuolating agent," an old name for the prototype polyomavirus, simian virus 40 (SV40).  The family of Papovaviridae is no longer used in recent taxonomy, but is split into the Papillomaviridae and the Polyomaviridae Papovaviruses

3. Virions are non enveloped, spherical in outline, with icosahedral symmetry. Virions are 55 (genus Papillomavirus) or 45 (genus Polyomavirus) nm in diameter The genome : circular double stranded DNA. The DNA has covalently closed ends , is circular and supercoiled and is infectious 8 (genus Papillomavirus)or 5 (genus Polyomavirus) kbp in size. Members of both genera replicate in nucleus Members of the genus Polyomavirus grow in cultured cells whereas, members of the genus Papillomavirus have not been grown in culture .

4. During replication, polyomavirus DNA is transcribed from both strands , whereas papillomavirus DNA is transcribed from one strand. Viruses encode proteins that promote cell growth by binding to the cellular growth-suppressor proteins p53 and p105RB. Viruses can cause lytic infections in permissive cells but cause abortive, persistent, or latent infections in non permissive cells. Note: Permissive cells are cells that can support the growth of a virus.

5. Replication Virions attach to cellular receptors, enter via receptor-mediated endocytosis, and are transported to the nucleus where they are uncoated, releasing their DNA. During productive infection , transcription of the viral genome is divided into early and late stages . Transcription of early and late coding regions is controlled by separate promoters and occurs on opposite DNA strands in the case of polyomaviruses and on the same strand with papillomaviruses.

6. First, the half of the genome that contains the early genes is transcribed, forming mRNAs that direct the synthesis of enzymes involved in viral replication. Late mRNAs that direct the synthesis of virion structural proteins are transcribed from the other half of the viral genome after DNA synthesis has begun. Progeny DNA molecules serve as additional template, amplifying the production of structural proteins greatly. Several different translational strategies are employed to enhance the limited coding capacity of the viral genomes.

7. Papovavirus DNA replication begins at a single unique origin of replication and proceeds bidirectional. Virions are assembled in the nucleus and are released on cell death, often just as a consequence of cellular replacement in epithelia. Some cells exhibit a characteristic cytopathic effect, marked by cytoplasmic vacuolization. An infected cell may produce 10,000 to 100,000 virions.

8. Human Papilloma Virus (HPV)

9. HPV infection is highly species/tissue specific, infecting only the cutaneous and mucosal epithelia of the anogenital tract (Angiogenital tract is a term used to refer to both the anus and genital tract) or upper respiratory tract . Transmission of HPV is believed to be through minor abrasions of the epithelium which expose cells in the basal layer for viral entry. Although heparin sulfate is suggested to be the mediator for the initial viral entry, the identity of the HPV receptor is still unknown. Primary HPV infection always begins in the cells of the basal layer of squamous epithelium, where the virus maintains its genome as low-copy episomal DNA.

10. HPV late gene expression and virion production only occur in the nucleus of terminally differentiated keratinocytes. (A keratinocyte is the predominant cell type in the epidermis, the outermost layer of the skin, constituting 90% of the cells found there.) Hence the vegetative HPV DNA production is tightly controlled by keratinocyte differentiation.

11. The circular double-stranded DNA genome of HPV, about 8 kb in size, is composed of three regions: a non-coding upstream regulatory region (URR) containing transcription promoters and DNA replication elements ; an early region encoding six proteins (E1, E2,E4, E5, E6 and E7 ); and a late region encoding two capsid proteins (L1 and L2).

12. Most HPV genes are transcribed as polycistronic mRNAs from a single DNA strand. HPV uses alternate RNA splicing and alternative RNA polyadenylation to ensure the proper expression of all open reading frames (ORFs) from a compact genome. Most HPV infections (90%) go away by themselves within two years.

13. If HPV infections persists , can cause a variety of serious health problems that include: Genital warts. Recurrent Respiratory Papillomatosis (RRP), a rare condition in which warts grow in the throat. Cervical cancer. Other, less common, but serious cancers, including genital cancers (cancer of the vulva, vagina, penis, or anus), and a type of head and neck cancer called oropharyngeal cancer (cancer in the back of throat, including the base of the tongue and tonsils).

14. Based on their oncogenic capability , papillomaviruses are divided into high-risk and low- risk groups . The high-risk groups consists of HPV-16, 18, 31, 33, 35, 39, 45, 51,52, 56, 58, 59 ,66. low-risk groups includes HPV-6 and 11.

15. There are more than 100 types of human papillomavirus (HPV). About 40 kinds can infect your genital area - vulva, vagina, cervix, rectum, anus, penis, and scrotum — as well as your mouth and throat. These kinds of HPV are spread during sexual contact. (Other types of HPV cause common warts like hand warts and plantar warts on the feet — but these aren’t sexually transmitted.) Genital HPV infections are very, very common.

16. In fact, most people who have sex get the HPV at some point in their lives. Most people with HPV have no symptoms and feel totally fine, so they usually don’t even know they’re infected. Most genital HPV infections aren’t harmful at all and go away on their own. But some kinds of HPV can lead to genital warts or certain types of cancer. Two types of HPV (types 6 and 11) cause most cases of genital warts. But they’re considered low-risk HPV because they don’t lead to cancer or other serious health problems.

17. At least a dozen types of HPV can sometimes lead to cancer, though two in particular (types 16 and 18) lead to the majority of cancer cases. These are called high-risk HPV. Cervical cancer is most commonly linked to HPV, but HPV can also cause cancer in vulva, vagina, penis, anus, mouth, and throat.

18. LESIONS IN HUMANS CAUSED BY HPVs LESIONS HPV TYPE COMMENT Plantar warts 1 Common warts 2, 27, 29, 54; 4 Flat warts 3, 10, 28, 41 Butcher’s warts 7, 40 Common warts on the hands of butchers Reddish brown (macular) plaques of epidermodysplasia verruciformis 5, 8, 12, 14, 19-23, 25, 36, 46, 47, 49; 9, 15, 17; 37, 38; 24 May become malignant in light- exposed areas Anogenital warts (condyloma); laryngeal papillomas 6, 11 Anogenital warts (vagina, vulva, rarely the cervix, penis, anus, perineum) are a commonly transmitted disease; respiratory papillomatosis, with malignant transformation, is a rare disease probably acquired at birth. Cervical intraepithelial neoplasia (CIN) and cervical cancer strong association moderate association 16, 18 31, 33, 35, 45, 51, 52, 56 Lower genital tract cancers

19. Reservoirs Humans (only reservoir) Transmission  Direct contact  Sexual  Perinatal  Contaminated fomites

20. Diseases Common Cutaneous Warts - “Verrucae vulgaris” Painless superficial medium-sized rough hyperkeratinized nodules at the site of initial infection. Primarily occurs on the hands and fingers as well as on the feet May progress to deep palmo-plantar warts. Cervical Intraepithelial Neoplasia “CIN” Benign neoplasm of the cervix May progress to cervical carcinoma Cervical Carcinoma Malignant neoplasm of the cervix Caused by progression of cervical intraepithelial neoplasia

21. Deep Palmo-Plantar Warts “Myrmecias” Painful deep medium-sized rough hyperkeratinized pigmented nodules at the site of initial infection. Primarily occurs on the feet and toes as well as on the hands Caused by progression of common cutaneous warts Anogenital Warts - “Condyloma acuminata” Multiple small papules coalescing to form a large cauliflower-like lesion at the site of initial infection. Primarily occurs on the external genitalia or perirectally

22. Diagnosis

23. T r e a t m e n t Topical liquid nitrogen (if common cutaneous warts, deep palmoplantar warts and/or anogenital warts).

24. Prevention Two vaccines (Cervarix and Gardasil) protect against cervical cancers. One vaccine (Gardasil) also protects against genital warts and cancers of the anus, vagina and vulva. Both vaccines are available for females, whereas Gardasil is available for males

25. Polyomaviridae Polyomaviruses (JCV and BKV)

26. PolyomaVirus Poly = multiple & oma = tumor Circular genome of dsDNA. Family: Polyomaviridae (formally grouped with papillomaviruses) Non-Enveloped, Naked Capsid. Icosahedral shape. Capsid: about 45nm(40-50nm) in diameter

27. The name polyoma refers to the virus’s ability to produce multiple ( poly) tumors (oma). Clinically, Polyomaviridae are relevant as they contribute to pathologies such as progressive multifocal leukoencephalopathy (JC virus), nephropathy (BK virus) and Merkel cell cancer (Merkel cell virus). murine Polyomavirus was the first Polyomavirus discovered by Ludwik Gross in 1953. Subsequently, many Polyomaviruses have been found to infect birds and mammals.

28. The Polyomaviruses have been extensively studied as tumor viruses in humans and animals, leading to fundamental insights into carcinogenesis, DNA replication and protein processing. Virus is probably acquired through the respiratory route spread by viremia to the kidneys early in life. Infections are asymptomatic Virus establishes persistent and latent infection in organs such as the kidneys and lungs .

29. Examples: 1-JC virus (JCV) /John Cunningham virus Causes progressive multifocal leukoencephalopathy ( PML ) Progressive demage or inflamation of white matter of brain at multiple locations. Harmless except in cases of weakend immune system in AIDS 2-BK virus (BKV) Latent until immunosuppression occurs. Causes renal diseases in kidney transplanted patients

30. BK virus (named for the patient’s initials): isolated in 1971 from the urine of a renal allograft recipient with ureteric obstruction JC virus (also named for the patient’s initials): cultivated in 1971 from the brain of a patient with progressive multifocal leukoencephalopathy in the context of Hodgkin's disease KI virus (“Karolinska Institutet”): identified 2007 using large-scale molecular virus screening method to identify unrecognized human pathogens. WU virus (“Washington University”): identified 2007 from respiratory secretions of patients with URI symptoms. MCV virus : found in Merkel cell carcinomas in 2008

31. Special Characteristics Persist as latent infections in a host without causing disease May produce tumor (Oncogenic)  Not the entire viral genome is transcribed in transformed cells but only the portion of it that encodes the early functions, that is, the various tumor antigens  There are three non-capsid regulatory proteins: large T (T Ag), small t and agnoprotein . Murine polyomaviruses have an additional middle T Ag.  (large T and small t antigens in the case of simian virus SV40 and large T, middle T and small t antigens in the case of polyoma virus)

32. These proteins are responsible for the induction and maintenance of the transformed state The large T antigen. the large T antigen stimulates host cell DNA synthesis , a function that can be separated from its ability to initiate viral DNA replication it is a transactive transcriptional activator capable of initiating the transcription of inappropriate cellular genes these binds to the two cellular anti oncogene proteins p53 and p110 Rb which inactivates their growth suppressor

33. Middle T antigen. Role in enhancing full expression of the transformed phenotype; expression of middle T antigen alone causes transformation to highly tumorigenic cells. Since polyoma middle T antigen by itself is capable of fully transforming cells, it is what is known as an acute transforming gene product Small t antigen. Complements the functions of large T. It causes loss of contact inhibition, ability to produce increased amounts of plasminogen activator and dissolution of intracellular actin cable network

34. The classification of Polyomaviruses is constantly evolving due to the explosion of newly discovered viruses. Previously, the family of Polyomaviridae was divided into three major clades; SV40 clade, avian clade and murine Polyomavirus clade. The recent reclassification by the International Committee on Taxonomy of Viruses (ICTV) has recommended three genera as follow: Many of the known viruses have not been fully classified or have not yet been officially accepted; hence, the taxonomy of this family is ongoing. Genus Types Species Orthopolyomavirus SV40 Wukipolyomavirus KI polyomavirus Avipolyomavirus Avian polyomavirus

35. Genome organization: Closed, Circular, dsDNA genome Complexed with cellular histones. Encodes proteins/genes: VP1(Viral protein 1), VP2, VP3---form viral capsid Polyomavirus replicates in nucleus of host, host dependent-specific

36. The genome is circular composed of double stranded DNA and encodes for 6 proteins; they are Large-T, small-T, viral protein 1 (VPl)/ viral protein 2 (VP2) and viral protein 3 (VP3) 1— and agnoprotein. The agnoprotein is a small multifunctional phosphor-protein found in the late coding part of the genome. It appears to be involved in DNA replication but the exact mechanism remains unclear. Agnoprotein is a protein expressed by some members of the polyomavirus family from a gene called the agnogene. Polyomaviruses in which it occurs include two human polyomaviruses associated with disease, BK virus and JC virus, as well as the simian polyomavirus SV40. It is about 5 kilobase pairs in length associated with cellular histones. VP 1-3 is responsible for the viral capsid formation.

37. Polyomaviruses are unenveloped double- stranded DNA viruses with circular genomes of around 5000 base pairs. The genome is packaged in a viral capsid of about 40-50 nanometers in diameter, which is icosahedral in shape.

38. The capsid is composed of 72 pentameric capsomeres of a protein called VP1, which is capable of self-assembly into a closed icosahedron; each pentamer of VP1 is associated with one molecule of one of the other two capsid proteins, VP2 or VP3. The genome of a typical polyomavirus codes for between 5 and 9 proteins, divided into two transcriptional regions called the early and late regions due to the time during infection in which they are transcribed. Each region is transcribed by the host cell's RNA polymerase II as a single pre-messenger RNA containing multiple genes. . The early region usually codes for two proteins, the small and large tumor antigens, produced by alternative splicing. The late region contains the three capsid structural proteins VP1, VP2, and VP3, produced by alternative translational start sites.

39. Replication and life cycle The polyomavirus life cycle begins with entry into a host cell. Cellular receptors for polyomaviruses are sialic acid residues of glycans, commonly gangliosides. The attachment of polyomaviruses to host cells is mediated by the binding of VP1 to sialylated glycans on the cell surface. In some particular viruses, additional cell-surface interactions occur; for example, the JC virus is believed to require interaction with the 5HT2A receptor and the Merkel cell virus with heparan sulfate. After binding to molecules on the cell surface, the virion is endocytosed and enters the endoplasmic reticulum the viral capsid structure is likely to be disrupted by action of host cell disulfide isomerase enzymes.

40. The details of transit to the nucleus are not clear and may vary among individual polyomaviruses. Virion particle is released from the endoplasmic reticulum into the cell cytoplasm, where the genome is released from the capsid, possibly due to the low calcium concentration in the cytoplasm. Both expression of viral genes and replication of the viral genome occur in the nucleus using host cell machinery. The early genes - comprising at minimum the small tumor antigen (ST) and large tumor antigen (LT) - are expressed first. These proteins serve to manipulate the host's cell cycle - dysregulating the transition from G1 phase to S phase, when the host cell's genome is replicated - because host cell DNA replication machinery is needed for viral genome replication.

41. Expression of the late genes results in accumulation of the viral capsid proteins in the host cell cytoplasm. Capsid components enter the nucleus in order to encapsidate new viral genomic DNA. New virions may be assembled in viral factories. The mechanism of viral release from the host cell varies among polyomaviruses; some express proteins that facilitate cell exit, such as the agnoprotein or VP4. In some cases high levels of encapsidated virus result in cell lysis, releasing the virions. Genus Host details Tissue t r opism Entry details R elease details R ep li c a t i on site As s e mbly site Transmission Polyomavirus Mammals; birds R e s pi r at o r y system; kidneys, brain Cell receptor endocytosis Lysis Nucleus Nucleus Oral-fecal

42. JC virus (JCV) life cycle in target cells. JCV adhesion to receptors in target cells. JCV internalization through clathrin mediated endocytosis and transport to the early endosomes. Transport to either recycling or late endosomes. Virus transport in the endoplasmic reticulum up to the nucleus. DNA replication in the nucleus. Early gene transcription (regulatory genes). Late gene transcription (structural genes). Translation of the transcripts from either early or late genes. Viral particles' assembly and virus release from target cells with either lytic (oligodendrocytes) or nonlytic mechanisms (tubular epithelial cells).

43. Transmission The mechanism of human-to-human transmission of the polyomaviruses JC virus (JCV) and BK Virus (BKV) has not been firmly established

44. Diseases Highly common childhood and young adult infections mostly cause little or no symptoms. Lifelong persistence among almost all adults Most common among persons who become immunosuppressed by AIDS, old age or after transplantation and include Merkel cell carcinoma (MCC) is a rare and highly aggressive skin cancer) , PML and BK nephropathy Progressive multifocal leukoencephalopathy caused by reactivation of JC virus Nephropathy (broad medical term used to denote disease or damage of the kidney) and Merkel cell cancer (Merkel cell virus) caused by reactivation of BK virus.

45. Merkel - cell carcinoma ( MCC ) is a rare and highly aggressive skin cancer, which, in most cases, is caused by the Merkel cell polyomavirus (MCV). a rare potentially fatal skin tumor affecting older and immunosuppressed individuals

46. Progressive multifocal leukoencephalopathy (PML) Progressive multifocal leukoencephalopathy (PML) is a deadly demyelinative disease of the CNS due to lytic infection of oligodendrocytes by the ubiquitous opportunistic polyoma virus JC(JCV) . It is a rare and usually fatal viral disease characterized by progressive damage (-pathy) or inflammation of the white matter (leuko-) of the brain (-encephalo-) at multiple locations (multifocal). It is caused by the JC virus, which is normally present and kept under control by the immune system. The JC virus is harmless except in cases of weakened immune systems.

47. Pathogenesis: The Polyomaviruses[JC virus (JCV), Bkvirus(BKV)and simian virus 40 (SV40)] establish subclinical and persistent infections and share the capacity for reactivation from latency in their host under immunosuppression. The JCV establishes latency mainly in the kidney and its reactivation results in the development of progressive multifocal leukoencephalopathy. The BKV causes infection in the kidney and the urinary tract.

48. Disease mechanism

49. Epidemiology: The members of the Polyomavirus are found throughout the world in birds, rodents, nonhuman primates, and of course, human populations. SV40 infects only Old World monkeys, and African and Indian macaques, but interestingly not New World monkeys (e.g., owl and squirrel monkeys). Perhaps indicating a species barrier that is not completely understood. The epidemiologic data have been collected mostly on the BKV and JCV because they are of human origin and cause widespread infections globally.

50. Serological surveys of populations using hemagglutination inhibition assays for the detection of antibodies indicates that seroconversion to BKV takes place early in life, 5 to 7years, with conversion to JCV occurring later. The virus is very common in the general population, infecting 70% to 90% of humans; most people acquire Human polyomavirus 2 in childhood or adolescence. It is found in high concentrations in urban sewage worldwide, leading some researchers to suspect contaminated water as a typical route of infection

51. Laboratory Diagnosis of Polyomavirus (JC and BK Infections) TEST DETECTS Pap smear of urinary epithelial cells Viral inclusions Electron microscopy Virions Immunofluorescence and immunoperoxidase staining Viral antigens DNA probe analysis Viral nucleic acids Nucleic acid hybridization in clinical specimens BK and JC viruses Nucleic acids Cell culture Human diploid lung fibroblasts Primary human fetal glial cells Virus isolation-BK Virus isolation-JC Pap smear of urinary epithelial cells Viral inclusions

52. Diagnosis Serum or urine PCR Urine cytology Biopsy Electron microscopy of biopsy or urine Screening by urine cytology or PCR recommended Every three months for first 2 years post transplant With graft dysfunction With all biopsies

53. Diagnosis: Urine Cytology Decoy Cells http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A74503

54. Histologic Diagnosis Viral Inclusions http://www.cap.org http://tpis1.upmc.com:81/tpis/GU/G00011a.html

55. Diagnosis: Immunohistochemistry http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A74503 Staining for SV40

56. Diagnosis: In Situ Hybridization http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A74503

57. Diagnosis: Electron Microscopy A) Free viral particles (~45 nm diameter) shed in the urine. B) Polyoma Allograft Nephropathy: 3D, cast-like polyomavirus aggregates (‘Haufen’) in urine are diagnostic of intra-renal disease. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A74503

58. T r e a t m e n t No known treatment However, it appears that some of fluoroquinolones may have therapeutic potential. Prevention Non available Adjustment of Immunosuppression Cidofovir Leflunomide

59. SV40 SV40 replicates in the kidneys of monkeys without causing disease, but can cause cancer in rodents under laboratory conditions. In the 1950s and early 1960s, well over 100 million people may have been exposed to SV40 due to previously undetected SV40 contamination of polio vaccine, prompting concern about the possibility that the virus might cause disease in humans. Although it has been reported as present in some human cancers, including brain tumors, bone tumors, mesotheliomas, and non-Hodgkin's lymphomas, accurate detection is often confounded by high levels of cross-reactivity for SV40 with widespread human polyomaviruses. Most virologists dismiss SV40 as a cause for human cancers

60. Species Virus name Abbreviation Human polyomavirus 5 Merkel cell polyomavirus MCPyV Human polyomavirus 8 Trichodysplasia spinulosa polyomavirus TSPyV Human polyomavirus 9 Human polyomavirus 9 HPyV9 Human polyomavirus 12 Human polyomavirus 12 HPyV12 Human polyomavirus 13 New Jersey polyomavirus NJPyV Human polyomavirus 1 BK polyomavirus BKPyV Human polyomavirus 2 JC polyomavirus JCPyV Human polyomavirus 3 KI polyomavirus KIPyV Human polyomavirus 4 WU polyomavirus WUPyV Human polyomavirus 6 Human polyomavirus 6 HPyV6 Human polyomavirus 7 Human polyomavirus 7 HPyV7 Human polyomavirus 10 MW polyomavirus MWPyV Human polyomavirus 11 STL polyomavirus STLPyV Human polyomavirus 14 Lyon IARC polyomavirus LIPyV